President Barack Obama stands with Jeh Johnson, his choice for the next Homeland Security Secretary, in the Rose Garden at the White House in Washington, Friday. Johnson was general counsel at the Defense Department during the wars in Iraq and Afghanistan.

President Obama’s choice of Jeh Johnson to lead the Department of Homeland Security comes at critical time for an agency struggling to replace old Coast Guard ships, boost border security, and deploy cybersecurity for the nation’s power grid and other critical infrastructure – all on a shrinking budget.

As general counsel for the Defense Department, Mr. Johnson has been in the middle of a raft of major issues facing the Obama presidency, from the ethics and legality of US drone strikes, to the status of gays in the military, to efforts to close the Guantanamo Bay prison. He signed off on all major military initiatives.

Johnson served President Bill Clinton as general counsel of the Department of the Air Force. Prior to that, he was assistant US attorney in the Southern District of New York, working on public corruption cases. After completing his recent tour at Defense, Johnson returned last December to the New York law firm Paul, Weiss, Rifkind, Wharton & Garrison.

“When I directed my national security team to be more open and transparent about how our policies work and how we make decisions, especially when it comes to preventing terrorist attacks, Jeh was one of the leaders who spoke eloquently about how we meet today's threats in a way that are consistent with our values, including the rule of law,” the president said in making the nomination Friday afternoon in the Rose Garden.

In response to Mr. Obama’s nomination, Johnson said he could not resist the call to help out once more.

“I am a New Yorker, and I was present in Manhattan on 9/11, which happens to be my birthday, when that bright and beautiful day was – a day something like this – was shattered by the largest terrorist attack on our homeland in history,” he said in a brief comment after his nomination. “I wandered the streets of New York that day and wondered and asked, what can I do? Since then, I have tried to devote myself to answering that question.”

Johnson’ nomination is not without controversy. He was criticized following a speech at Oxford University last year when he remarked that the war on terror would not go on endlessly. At some “tipping point,” he noted, the military action against Al Qaeda would shift over to law enforcement and intelligence agencies.

“War must be regarded as a finite, extraordinary, and unnatural state of affairs,” Johnson said. “In its 12th year, we must not accept the current conflict, and all that it entails, as the new normal.”

However he also made remarks noting that the shift would not happen for some time yet.

Johnson has also been criticized for advancing legal justifications for the Obama administration’s policy on using drone strikes in the anti-terrorism effort. Even so, some human rights advocates applauded the nomination.

“As DHS Secretary, Johnson would have a leading role in ensuring that American law and practice upholds our country’s commitment to asylum and refugees,” Elisa Massimino, president of Human Rights First, said in a statement. “We urge Jeh Johnson to make this vulnerable population a priority as his nomination moves forward.”

On the flip side, one major thing going for Johnson as DHS chief is that he has already been vetted and approved once by the Senate for his defense post, several observers said.

He’s also used to cracking the whip, having led a crackdown on unauthorized leaks in the Defense Department, much criticized by whistleblower groups.

If confirmed, Johnson faces significant challenges that will require all his Defense Department experience and more. Under Obama’s watch the DHS has wrestled with the proper balance in it mission – how much to focus on counter-terrorism versus how much on the broader hazards like hurricanes and floods, homeland security experts say.

Getting that balance right will require balancing political pressure for, say, tougher border security – with the need for deep investments that can respond to natural disasters. Johnson will need to be good at wooing companies that own much of the nation’s critical infrastructure to participate in defending it, the experts say.

Ironically, the DHS – more than a decade after it was created by merging nearly two dozen federal agencies in the wake of 9/11 – is still trying to define its role in defending the nation against terrorism. After the Boston Marathon terrorist bombing, the first such event since 9/11, the nation found itself listening mostly to local police chiefs, FBI representatives, and the president, while the DHS was responding in a coordinating role out of sight.

“The DHS was really invisible after the Boston terror bombings,” Stephen Flynn, director of the Kostas Research Institute for Homeland Security at Northeastern University. “This was the first terror attack like this since 9/11 and nobody thought to ask – where’s homeland security?”

“Obviously he’s got a strong background in weighty issues of the war on terror,” Dr. Flynn says of Johnson. “What will challenge him at DHS is that most of the heavy lifting in protecting the nation is really at the state and local level – and in somehow getting the private sector that operates critical infrastructures that are particularly vulnerable to go along with measures needed to increase security.”

If confirmed, Mr. Johnson faces a department with a squeaky tight budget at a time of high demand.

“The challenge to reduce the US deficit has placed a strain on the DHS's, as well as other government departments', ability to properly fund all critical agencies,” concluded an analysis last month by the consulting firm Frost & Sullivan. “Although not to the point of dysfunction, the agencies are forced to operate at a lesser efficiency and with fewer personnel.”

Some agency divisions, like the DHS Directorate of Science and Technology, are responsible for developing and deploying new communications and sensor technologies to defend the nation. Yet that office’s budget has been heavily cut, Flynn notes.

Right now, for instance, the US needs new radiological alarms and sensors at the nation’s ports with the old, first generation equipment deployed after 9/11 wearing out. The DHS is also still struggling with a congressional requirement to deploy biometric sensors at the nation’s airports and other exit points. But how to do that effectively on a tight budget is a big question.